From 9c704ecd2ba1a01f0b82d0f1ea6d9d3e3011fff7 Mon Sep 17 00:00:00 2001
From: Diane Trout <diane@caltech.edu>
Date: Thu, 6 Sep 2007 23:29:13 +0000
Subject: [PATCH] attach annotations property to seq_span

---
 py/annotations.cpp         |  7 +++----
 py/seq_span.cpp            |  2 ++
 py/test/TestAnnotations.py |  4 ++--
 py/test/TestSeqSpan.py     | 12 ++++++++++++
 4 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/py/annotations.cpp b/py/annotations.cpp
index 453406d..1418089 100644
--- a/py/annotations.cpp
+++ b/py/annotations.cpp
@@ -33,7 +33,7 @@ void export_annotations()
 {
   to_python_converter<pair_string, pair_string_to_tuple>();
 
-  class_<Annotations>("annotations", init<std::string>())
+  class_<Annotations>("Annotations", init<std::string>())
     .add_property("name", &Annotations::name, &Annotations::setName)
     .def("__contains__", &map_item<Annotations>::in)
     .def("__delitem__", &map_item<Annotations>::del)
@@ -45,8 +45,7 @@ void export_annotations()
     .def("keys", &map_item<Annotations>::keys)
     .def("values", &map_item<Annotations>::values)
     .def("items", &map_item<Annotations>::items)
+  ;
 
-    ;
-
-  //register_ptr_to_python< AnnotationsRef >();
+  register_ptr_to_python< AnnotationsRef >();
 }
diff --git a/py/seq_span.cpp b/py/seq_span.cpp
index d3e0b5b..74e6244 100644
--- a/py/seq_span.cpp
+++ b/py/seq_span.cpp
@@ -52,6 +52,8 @@ void export_seq_span()
     //.add_property("alphabet", 
     //              make_getter(&SeqSpan::get_alphabet,
     //                          return_value_policy<copy_const_reference>()))
+    .add_property("annotations", &SeqSpan::annotations, 
+                                 &SeqSpan::setAnnotations)
     .add_property("start", &SeqSpan::start, &SeqSpan::setStart,
                   "start position relative to root sequence")
     .add_property("stop", &SeqSpan::stop, &SeqSpan::setStop,
diff --git a/py/test/TestAnnotations.py b/py/test/TestAnnotations.py
index 6c432bd..ec254ec 100644
--- a/py/test/TestAnnotations.py
+++ b/py/test/TestAnnotations.py
@@ -10,7 +10,7 @@ import mussa
 class TestAnnotations(unittest.TestCase):
   def testSimple(self):
     name_value = 'name_value'
-    a = mussa.annotations(name_value)
+    a = mussa.Annotations(name_value)
     self.failUnlessEqual( a['name'], name_value)
     self.failUnlessEqual( len(a), 1)
     self.failUnlessEqual( a.keys(), ['name'])
@@ -18,7 +18,7 @@ class TestAnnotations(unittest.TestCase):
 
   def testIter(self):
     name_value = 'name_value'
-    a = mussa.annotations(name_value)
+    a = mussa.Annotations(name_value)
     l = [ x for x in a ]
     self.failUnlessEqual(len(l), 1)
     self.failUnlessEqual(l[0], ('name', 'name_value'))
diff --git a/py/test/TestSeqSpan.py b/py/test/TestSeqSpan.py
index de10824..3a56d92 100644
--- a/py/test/TestSeqSpan.py
+++ b/py/test/TestSeqSpan.py
@@ -42,6 +42,18 @@ class TestSeqSpan(unittest.TestCase):
   #  self.failUnless(sparent is s1.parent())
   #  self.failUnlessEqual(sparent == s1.parent())
 
+  def testAnnotations(self):
+    seq_text = "AAAAAG"
+    name = "As"
+    s = mussa.SeqSpan(seq_text)
+    s.annotations = mussa.Annotations(name)
+    self.failUnlessEqual(s.annotations.name, name)
+    self.failUnlessEqual(s.annotations['name'], name)
+
+    term_key = 'GO term'
+    term = "term"
+    s.annotations[term_key] = term
+    self.failUnlessEqual(s.annotations[term_key], term)
 
 def suite():
   return unittest.makeSuite(TestSeqSpan, 'test')
-- 
2.30.2